AMBER: average structure

From: emilia wu <>
Date: Mon, 20 Jun 2005 08:15:53 +0800

Dear Amber users,

I have done 1ns simulation with explicit water model, and I want to get the average structure after equilibration from 50ps to 500ps using ptraj (amber8) using the input below.
After I load the average.pdb into leap to get the prmtop file, i got a lot of warnings like this:

WARNING: There is a bond of 0.049558 angstroms between:
------- .R<GLU 84>.A<CA 3> and .R<GLU 84>.A<CB 5>
WARNING: There is a bond of 0.230554 angstroms between:
------- .R<GLU 84>.A<CA 3> and .R<GLU 84>.A<C 14>
WARNING: There is a bond of 0.035128 angstroms between:
------- .R<GLU 84>.A<N 1> and .R<GLU 84>.A<H 2>

I copied several lines here, and the full leap.log is in the attachment. I also get some other snapshots from the mdcrd file, when i loaded these files into leap, no warnings was given.

ptraj input:

trajin comp_wat_md.mdcrd 251 2500
center :1-277
image center familiar
strip :WAT
strip :Cl-
average average.pdb pdb

Is it because of my ptraj script? Please give me some suggestions. Thank you very much.


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Received on Mon Jun 20 2005 - 01:53:00 PDT
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